To be honest, after seeing someone point out Megatrons Derpy eye, I went back to watch the episode and yeah it seems a little off centered, but barely. However, I noticed with Megs and Bulkhead their eyes are pretty far apart ratio wise to their face, so maybe it's no mis-aligned pupils so much as it's a trick of our own eyes tripping out at the odd face ratios.

To be fair the animators are probably in a constant crunch to get the episodes finished and with a certain level of quality. The eyes don't really bother me, in fact I don't even think there is a problem... they are SUPPOSED to look like that, they seem fine to me.

The only Eyes that bother me is Bumblebee's because I preffered when they were just big black holes in the middle with a blue ring and not with the Blue Pupil... I thought that looked cooler for his design. Of course that in itself WAS an error, becasue in the first episode he had the dots, then they went away.... and then they came back again.

everyone else has a flat face and their eyes closer together. because their eyes are also a little bit on the side of their head, from the side we see more of an eye, making the derp effect. its an illusion.